basic question re. new variants found

[nat38]

so after a sequencing project I have a small list of variants called (chr and position) - what is the best/easiest/fstest way to check whether they are syn, non-syn, stop codons, etc?

many thanks!

[rjohnp]

http://wannovar.usc.edu/ is a good server for this. It will also annotate a plethora of other details such as the predicted damaging nature of non-synonymous changes (polyphen etc.) as well as minor allele frequencies if it is a known variant.

[nat38]

thanks for this!
just tried but seem to have problems with the input format - would you mind giving me an example of your input files? thanks a lot

[rjohnp]

http://www.openbioinformatics.org/annovar/annovar_input.html

As well as the positional (1 based) information, you also need to give it the reference and observed genotypes, tab delimited.

Chr 5' 3' Ref Alt

It can also take VCF formats pasted in, if you have it in that.

[nat38]

thanks again, that's exactly waht I am using as input file but for whatever reason the output comes back empty?

[rjohnp]

I just tried:

17 7918018 7918018 C T

and that seemed to work fine, if you're using this format, make sure to select 'ANNOVAR input format' for the input format.

If this does still not work http://provean.jcvi.org/genome_submit.php is a similar thing, though it doesn't do allele frequencies and all that.

[nat38]

weird, managed to get results with wANNOVAR, but can't get Provean to work now!

[rjohnp]

weird, managed to get results with wANNOVAR, but can't get Provean to work now!

Don't you just love technology, wANNOVAR gives you SIFT scores anyway I believe, plus all the rest, so the better out of the two to have working at least.

Amazing how the hardest part of bioinformatics seems to be just getting files in the right formats, seems to be half the job.